After Dr. Brainstorm's most prestigious project yet, the Doom Satellite (which tampers with several other satellites), is utterly wrecked by Calvin and company (because he shut down DirectTV's satellite), a stray laser blast from the battle ricochets towards Earth, unknown to anyone...

It burrows through pavement and dirt and eventually hits a shiny chrome sphere, releasing aKiller Robot - Shadow. Newly awakened, he rushes off to a cold landscape, where he goes into an abandoned lair, awakeninganotherevil trapped in stasis - Thunderstorm, his master. Bemoaning post-stasis trauma, he switches on the lab, upon which he finds out he's been sealed for five years because of Dr. Brainstorm.

As Calvin holds a secret GROSS meeting with Hobbes in his room (thanks to Rosalyn), Dr. Brainstorm returns to his lab defeated. Before he can leave to think of Super Plan B, he gets a call. It's Thunderstorm and Shadow, shocking the heck out of both him and Jack. The message contains little more than a declaration that he's going to Take Over the World. When it finishes, Brainstorm immediately starts ranting and raving about him, before suggesting they build a Trojan Horse to fool him. Jack figures that he'd probably need Calvin and Hobbes' help, but...

Jack: Right. Now how about you tell me why it is that when you need help, you refuse it.

Brainstorm: Because I want to be the heroic villain, okay? There's got to be at least one time where I'm the one who has a victory!

Nonetheless, Jack teleports over to Calvin and Hobbes to discuss things with them. Via flashback, he reveals that the two had a pretty big rivalary going on since college - Thunderstorm was Always Someone Better to Brainstorm, until the latter accidentally trapped the former in stasis when he and his Killer Robot Shadow attempted to kill him and Jack.. Calvin gathers the rest of the gang, Hobbes vanishing as per usual.

Back at Thunderstorm's lab, Shadow's duplicator is shown for the first time. He gets a call from Brainstorm, whom he mocks. After he attempts to send one of the Shadows to assassinate him, the gang bust through the entrance of his lab to stop him. He sics a Shadow at them, which they easily defeat. Unfortunately, its clone is also a Technopath, and traps the boys with wires before the MTM saves them.

After some more battling, Shadow initiates the "Last Resort Robo-Launcher" - a huge swarm of tiny bugs that overwhelms the heroes, letting Thunderstorm imprison them. Calvin refuses to tell him anything, so Thunderstorm simply extracts every single bit of information from them. He then swipes Calvin's hypercube to force open a portal between dimensions so he can create a whole army of Shadows via placing more portals across the globe. Sherman frantically warns him that the results could be disastrous, but his concerns are dismissed, as he doesn't actually have a power source big enough to do so... until now. Yes, the Doom Satellite wasn't completely useless, its power enough to cover the planet, and he shortly blasts off into space.

Meanwhile, Rosalyn is unable to find Calvin, and when his parents get home, they call the police after finding something similar happened to Andy.

At the Doom Satellite, Thunderstorm has everything up and running, but his superweapon takes an hour to charge. Back in the cell, Andy uses the Scream Horn to destroy the Force Field, allowing Calvin to retrieve his inventions and the gang to take off.

In his lair, Brainstorm panics about the incoming Shadow, and refutes Jack's suggestion to simply leave the place - "EVERY MAN GOES DOWN WITH HIS SHIP!" When Jack questions this, he abruptly stops still in his tracks, not even his trademark Berserk Button snapping him out of it. He finally begins to resume preparing, and Jack decides to be useful and set up a Force Field around the lab. Unfortunately, that's not stopping Shadow from entering anyway, and though Brainstorm manages to escape him for a while with his Servant Ray, he's shortly pinned down. Luckily, Calvin and the gang show up in the nick of time to save him.

Brainstorm still refuses to allow them to help, but eventually he gives in. He sets up a laser, but a timely power failure stops it, and the backup power isn't enough. Calvin simply teleports them up to the space station's closet, where Thunderstorm immediately finds them. He and Shadow attack, and a large brawl ensues. Jack easily blocks Shadow - since his orders were to kill, a non-living organism doesn't count. Unfortunately, he ends up sliced in half.

Nonetheless, the gang ends up captured, and Thunderstorm soon enacts his world-domination plot. Several minor characters are captured by the Shadow clones, and Thunderstorm has no intention of closing the portal - unfortunately, by doing so, he'll eventually destroy both worlds.

Unfortunately, his victory is short-lived, as two Shadows take him captive as he tries to fire a blast, and Thunderstorm destroys the MTM with his Servant Ray.

Everyone is then forced to march single-file by the Shadow clones to a prison, where Calvin's and Brainstorm's inventions are confiscated, and everyone is thrown into their cells. Hobbes mocks Calvin's inventions, mostly the MTM, and Calvin abruptly steps on his tail, furious.

Calvin then transmogrifies a brick into the Servant Ray, and he manages to escape and free Brainstorm and Jack with it, neglecting the others.

Meanwhile, Thunderstorm tries to open the portal even wider (neglecting to stabilize it) when he finds out they've escaped. He and Shadow teleport back down to Earth, where Calvin and Sherman are trying to fix the MTM. Shortly after, Hobbes picks up the Transmogrifier Gun - "better dead than a jerk". Needless to say, it's on.

While the brawl rages on, Calvin and Sherman manage to get the MTM back to working condition, but Thunderstorm and Shadow have handily defeated the others. Thankfully, the MTM manages to activate his Energy Absorber (now completely repaired) to send the Shadow clones back to their home dimension. He then sends everyone (save Thunderstorm and Shadow, who teleport back up to the Space Station) back in time, after the first outage.

Brainstorm: Well, Calvin, you have proven to be a most worthy advisory.

However, Thunderstorm and Shadow teleport them to the space station once more, the former yelling at them for destroying his life's dreams and pulling out his Servant Ray. Everyone braces for death...

... when Dr. Brainstorm shoots the gun out of his hand with his own Servant Ray. This begins a fight between them and Shadow, ending when the MTM manages to activate the Self-Destruct Mechanism. Everyone but Thunderstorm and Shadow runs to the last Escape Pod, riding the shockwave of the ensuing explosion.

Safe at last, Brainstorm acts like his old self once more, and the heroes go to watch their movie again.

Meanwhile, a severely injured Thunderstorm and Shadow make it back to their lair... but they end up frozen once more.

Thunderstorm: Success! Now we have absolute threat! Excellent! The place can actually do some evil-like damage now! Every glitch is finally repaired! The gamma-rays are fully-loaded, the laser-cannons are set, the navicomp is functional, and the cappuccino machine has bendy straws! I'M IN THE GROOVE AGAIN!

Foreshadowing: The MTM takes a while to process, earning the ire of the gang, along with Hobbes' cowardice. When the latter mocks the deceased former as useless, Calvin is infuriated and belts out a "The Reason You Suck" Speech.

At one point, the MTM complains about his low battery, which prevents him from teleporting everyone from the station.

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